庆阳市本土新冠病毒Omicron变异株的全基因组特征分析  

Genome-wide Characterization of Omicron Variants of Local COVID-19 in Qingyang,China

作　　者：朱圭娜[1] 王文军[1] 侯怀哲 景永峰 李保娣[3] 辛奇 ZHU Guina;WANG Wenjun;HOU Huaizhe;JING Yongfeng;LI Baodi;XIN Qi(Laboratory Department of Qingyang Center for Disease Control and Prevention,Qingyang 745000,China;Qingyang People's Hospital,Qingyang 745000,China;Gansu Provincial Center for Disease Control and Prevention,Lanzhou 730000,China;School of Basic Medicine,LanzhouUniversity,Lanzhou730000,China)

机构地区：[1]庆阳市疾病预防控制中心,庆阳745000 [2]庆阳市人民医院,庆阳745000 [3]甘肃省疾病预防控制中心,兰州730000 [4]兰州大学基础医学院,兰州730000

出　　处：《病毒学报》2023年第3期654-660,共7页Chinese Journal of Virology

基　　金：甘肃省卫生健康行业科研项目(项目号:GSWSQN2021-012),题目:庆阳市流感和禽流感病毒的流行病学及病原学分子特征研究;甘肃省青年科技基金计划项目(项目号:21JR7RM909),题目:探讨IL-28B基因多态性与庆阳地区丙型肝炎易患性的关系及丙型肝炎实验室检测的方法学评价。

摘　　要：本文将高通量测序技术应用于新型冠状病毒感染(COVID-19)的疫情防控当中,从基因组水平上了解新型冠状病毒(SARS-CoV-2)的分子学特征及变异情况,从而为疫情的防控提供科学的参考及准确的研判依据。我们选取2022年8月-9月庆阳市报告的新冠疫情本土感染者标本作为研究对象,对标本进行核酸检测和病毒全基因组测序并进行序列比对,使用MEGA分析软件基于邻接法构建病毒进化树,从而了解病毒的分子学特征及相关性。本研究所选取的9例病例均为普通型病例,核酸检测Ct值均较低。Nextclade分型结果显示:9条序列均属于21L型Omicron变异株;Pangolin分型结果显示:9条序列均处于Pangolin谱系中的BA.2.76进化分支上。与武汉参考株Wuhan-Hu-1(NC_045512.2)相比,9条SARS-CoV-2序列的核苷酸同源性中位数为94.6%,核苷酸突变类型包括76~78个替换突变和3处缺失突变,氨基酸突变位点共涉及10个基因编码框,按氨基酸错义突变总数由多到少依次为:S蛋白区,ORF1ab区,N蛋白区,M蛋白区,E蛋白区和ORF3a、ORF6、ORF8、ORF9b区。进化分析结果显示:本研究获得的9条SARS-CoV-2全基因组序列处于Omicron变异株BA.2.76谱系。SARS-CoV-2在流行传播过程中,不断出现传播能力增强、抗体有效性降低及免疫逃避的新毒株,未来也将可能出现新的变异株,庆阳市首次将高通量测序技术应用到新冠病毒感染的疫情防控当中,从基因组水平上了解病毒的分子学特征,对监测庆阳市疫情防控及准确的研判具有重要意义。In this paper,we applied high-throughput sequencing in the epidemic prevention and control of Coronavirus disease 19(COVID-19)to understand the molecular characteristics and variations of SARS-CoV-2 at the genomic level,so as to provide scientific reference and accurate analysis for the prevention and control of outbreaks.We selected specimens of SARS-CoV-2 infected patients reported in Qingyang,China from August to September 2022 as research subjects.The specimens were tested for nucleic acid,viral whole-genome sequencing and sequence alignment.The MEGA analysis software was used to construct a virus evolutionary tree based on the adjacent method to understand the molecular characteristics and correlation of viruses.All the 9 patients selected in this study were common cases with low Ct values.The Nextclade subtyping results showed that all the 9 sequences belonged to type 21L Omicron variant.The Pangolin subtyping results showed that all 9 sequences were on the BA.2.76 evolutionary branch.Compared with the Wuhan reference strain Wuhan-Hu-1(NC.045512.2),the median of nucleotide homology of 9 SARS-CoV-2 sequences was 94.6%.The types of nucleotide mutations included 76-78 substitution mutations and 3 deletion mutations.Amino acid variant sites involved 10 gene coding frames.The total number of amino acid missense mutations ranked from more to less were S protein region,ORFlab region,N protein regions,M protein regions,E protein region and one each for ORF3a,ORF6,ORF8 and ORF9b regions successively.The results of the evolutionary analysis showed that 9 SARS-CoV-2 whole-genome sequences obtained in this study are in the Omicron variant BA.2.76 lineage.In the process of epidemic spread of SARS-CoV-2,there were continuous emergence of new strains with enhanced transmission capacity,reduced antibody effectiveness and immune evasion.New variants will also be possible in the future.The high-throughput sequencing was applied for the epidemic prevention and control of SARS-CoV-2 for the first time in Qingyang,China which m

关 键 词：新型冠状病毒 奥密克戎 全基因组测序 分子特征 

分 类 号：R373.1[医药卫生—病原生物学]